/codiversification

Code and notes for the Ley Lab's codiversification paper.

Primary LanguageJupyter Notebook

Codiversification Project

This complilation of code and notes reproduces the results of the Ley Lab's codiversification paper:

Codiversification of gut microbiota with humans. Taichi A. Suzuki, Liam Fitzstevens, Victor T. Schmidt, Hagay Enav, Kelsey Huus, Mirabeau Mbong, Bayode R. Adegbite, Jeannot F. Zinsou, Meral Esen, Thirumalaisamy P. Velavan, Ayola A. Adegnika, Le Huu Song, Timothy D. Spector, Amanda L. Muehlbauer, Nina Marchi, Ran Blekhman, Laure Ségurel, Nicholas D. Youngblut, Peter Kremsner, Ruth E. Ley. bioRxiv 2021.10.12.462973; doi: https://doi.org/10.1101/2021.10.12.462973

The number prefix reflects the general order in which the code is executed.

Data

  • Illumina metagenome sequence data
    • The raw sequence data are available from the European Nucleotide Archive under study accession number PRJEB46788
  • Other
    • Other associated data is provided as supplemental material in the published manuscript